2D Clusterless Decoding

2D Clusterless Decoding¶

In [ ]:

%reload_ext autoreload
%autoreload 2

%reload_ext autoreload %autoreload 2

In [2]:

# ignore datajoint+jupyter async warnings
import warnings

warnings.simplefilter("ignore", category=DeprecationWarning)
warnings.simplefilter("ignore", category=ResourceWarning)

# ignore datajoint+jupyter async warnings import warnings warnings.simplefilter("ignore", category=DeprecationWarning) warnings.simplefilter("ignore", category=ResourceWarning)

In [3]:

import matplotlib.pyplot as plt
import numpy as np
import xarray as xr
import logging

FORMAT = "%(asctime)s %(message)s"

logging.basicConfig(level="INFO", format=FORMAT, datefmt="%d-%b-%y %H:%M:%S")

import matplotlib.pyplot as plt import numpy as np import xarray as xr import logging FORMAT = "%(asctime)s %(message)s" logging.basicConfig(level="INFO", format=FORMAT, datefmt="%d-%b-%y %H:%M:%S")

In [4]:

nwb_copy_file_name = "chimi20200216_new_.nwb"

nwb_copy_file_name = "chimi20200216_new_.nwb"

In [5]:

from spyglass.decoding.clusterless import UnitMarksIndicator


marks = (
    UnitMarksIndicator
    & {
        "nwb_file_name": nwb_copy_file_name,
        "sort_interval_name": "runs_noPrePostTrialTimes raw data valid times",
        "filter_parameter_set_name": "franklab_default_hippocampus",
        "unit_inclusion_param_name": "all2",
        "mark_param_name": "default",
        "interval_list_name": "pos 1 valid times",
        "sampling_rate": 500,
    }
).fetch_xarray()

marks

from spyglass.decoding.clusterless import UnitMarksIndicator marks = ( UnitMarksIndicator & { "nwb_file_name": nwb_copy_file_name, "sort_interval_name": "runs_noPrePostTrialTimes raw data valid times", "filter_parameter_set_name": "franklab_default_hippocampus", "unit_inclusion_param_name": "all2", "mark_param_name": "default", "interval_list_name": "pos 1 valid times", "sampling_rate": 500, } ).fetch_xarray() marks

/home/edeno/miniconda3/envs/spyglass/lib/python3.8/site-packages/seaborn/rcmod.py:82: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
  if LooseVersion(mpl.__version__) >= "3.0":
/home/edeno/miniconda3/envs/spyglass/lib/python3.8/site-packages/setuptools/_distutils/version.py:346: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
  other = LooseVersion(other)
13-Sep-22 15:42:32 Connected edeno@lmf-db.cin.ucsf.edu:3306

Connecting edeno@lmf-db.cin.ucsf.edu:3306

/stelmo/nwb/analysis/chimi20200216_new_7M0E8ERPE7.nwb
/stelmo/nwb/analysis/chimi20200216_new_6WW86B509M.nwb
/stelmo/nwb/analysis/chimi20200216_new_TLD0MCIC5H.nwb
/stelmo/nwb/analysis/chimi20200216_new_7BEQDOTX3E.nwb
/stelmo/nwb/analysis/chimi20200216_new_F8QVNUMVJS.nwb
/stelmo/nwb/analysis/chimi20200216_new_BVZKYWREUE.nwb
/stelmo/nwb/analysis/chimi20200216_new_3HMJON557D.nwb
/stelmo/nwb/analysis/chimi20200216_new_QGMZ5ESFVA.nwb
/stelmo/nwb/analysis/chimi20200216_new_1KRVBBCP2N.nwb
/stelmo/nwb/analysis/chimi20200216_new_9E2Z0R6TLO.nwb
/stelmo/nwb/analysis/chimi20200216_new_ALRF0STB1P.nwb
/stelmo/nwb/analysis/chimi20200216_new_F2TDZW8LRY.nwb
/stelmo/nwb/analysis/chimi20200216_new_LTEU71Z21T.nwb
/stelmo/nwb/analysis/chimi20200216_new_KT4E4LIYAI.nwb
/stelmo/nwb/analysis/chimi20200216_new_KOIRLX6R6X.nwb
/stelmo/nwb/analysis/chimi20200216_new_4S01EA6NVN.nwb
/stelmo/nwb/analysis/chimi20200216_new_ATQO860QOB.nwb
/stelmo/nwb/analysis/chimi20200216_new_H3E2HYMEJA.nwb
/stelmo/nwb/analysis/chimi20200216_new_4KJ4XVBKW3.nwb
/stelmo/nwb/analysis/chimi20200216_new_0V98T6HQHX.nwb
/stelmo/nwb/analysis/chimi20200216_new_A5FBXFDZMD.nwb
/stelmo/nwb/analysis/chimi20200216_new_A5ELOH1L7Y.nwb

Out[5]:

<xarray.DataArray (time: 655645, marks: 4, electrodes: 22)>
array([[[  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan]],

       [[  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan]],

       [[  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan]],

       ...,

       [[ -99.,   nan,   nan, ...,   nan,   nan,   nan],
        [-100.,   nan,   nan, ...,   nan,   nan,   nan],
        [ -94.,   nan,   nan, ...,   nan,   nan,   nan],
        [-104.,   nan,   nan, ...,   nan,   nan,   nan]],

       [[  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan]],

       [[  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan],
        [  nan,   nan,   nan, ...,   nan,   nan,   nan]]])
Coordinates:
  * time        (time) float64 1.582e+09 1.582e+09 ... 1.582e+09 1.582e+09
  * marks       (marks) <U14 'amplitude_0000' ... 'amplitude_0003'
  * electrodes  (electrodes) int64 0 1 2 3 5 6 7 8 9 ... 15 16 17 18 19 21 22 23

xarray.DataArray

• time: 655645
• marks: 4
• electrodes: 22

• nan nan nan nan nan -170.0 nan nan ... nan nan nan nan nan nan nan nan

  array([[[  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan]],
  
         [[  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan]],
  
         [[  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan]],
  
         ...,
  
         [[ -99.,   nan,   nan, ...,   nan,   nan,   nan],
          [-100.,   nan,   nan, ...,   nan,   nan,   nan],
          [ -94.,   nan,   nan, ...,   nan,   nan,   nan],
          [-104.,   nan,   nan, ...,   nan,   nan,   nan]],
  
         [[  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan]],
  
         [[  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan],
          [  nan,   nan,   nan, ...,   nan,   nan,   nan]]])

• Coordinates: (3)
  • time
    (time)
    float64
    1.582e+09 1.582e+09 ... 1.582e+09

    array([1.581887e+09, 1.581887e+09, 1.581887e+09, ..., 1.581888e+09,
           1.581888e+09, 1.581888e+09])

  • marks
    (marks)
    <U14
    'amplitude_0000' ... 'amplitude_...

    array(['amplitude_0000', 'amplitude_0001', 'amplitude_0002', 'amplitude_0003'],
          dtype='<U14')

  • electrodes
    (electrodes)
    int64
    0 1 2 3 5 6 7 ... 17 18 19 21 22 23

    array([ 0,  1,  2,  3,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
           19, 21, 22, 23])

• Attributes: (0)

In [6]:

plt.scatter(
    marks.isel(electrodes=0).dropna("time").isel(marks=0),
    marks.isel(electrodes=0).dropna("time").isel(marks=1),
    s=1,
)

plt.scatter( marks.isel(electrodes=0).dropna("time").isel(marks=0), marks.isel(electrodes=0).dropna("time").isel(marks=1), s=1, )

Out[6]:

<matplotlib.collections.PathCollection at 0x7f2ad72ae3a0>

In [7]:

from spyglass.common.common_position import IntervalPositionInfo


position_key = {
    "nwb_file_name": nwb_copy_file_name,
    "interval_list_name": "pos 1 valid times",
    "position_info_param_name": "default_decoding",
}

position_info = (IntervalPositionInfo() & position_key).fetch1_dataframe()

position_info

from spyglass.common.common_position import IntervalPositionInfo position_key = { "nwb_file_name": nwb_copy_file_name, "interval_list_name": "pos 1 valid times", "position_info_param_name": "default_decoding", } position_info = (IntervalPositionInfo() & position_key).fetch1_dataframe() position_info

/stelmo/nwb/analysis/chimi20200216_new_6YC9LPAR7S.nwb

Out[7]:

	head_position_x	head_position_y	head_orientation	head_velocity_x	head_velocity_y	head_speed
time
1.581887e+09	91.051650	211.127050	2.680048	1.741550	2.301478	2.886139
1.581887e+09	91.039455	211.144123	3.003241	1.827555	2.333931	2.964320
1.581887e+09	91.027260	211.161196	3.008398	1.915800	2.366668	3.044898
1.581887e+09	91.015065	211.178268	3.012802	2.006286	2.399705	3.127901
1.581887e+09	91.002871	211.195341	3.017242	2.099012	2.433059	3.213352
...	...	...	...	...	...	...
1.581888e+09	182.158583	201.299625	-0.944304	0.057520	-0.356012	0.360629
1.581888e+09	182.158583	201.296373	-0.942329	0.053954	-0.356343	0.360404
1.581888e+09	182.158583	201.293121	-0.940357	0.050477	-0.356407	0.359964
1.581888e+09	182.158583	201.289869	-0.953059	0.047091	-0.356212	0.359312
1.581888e+09	182.158583	201.286617	-0.588081	0.043796	-0.355764	0.358450

655645 rows × 6 columns

In [8]:

plt.plot(position_info.head_position_x, position_info.head_position_y)

plt.plot(position_info.head_position_x, position_info.head_position_y)

Out[8]:

[<matplotlib.lines.Line2D at 0x7f2ad70abfd0>]

In [9]:

position_info.shape, marks.shape

position_info.shape, marks.shape

Out[9]:

((655645, 6), (655645, 4, 22))

In [10]:

from spyglass.common.common_interval import interval_list_intersect
from spyglass.common import IntervalList

key = {}
key["interval_list_name"] = "02_r1"
key["nwb_file_name"] = nwb_copy_file_name

interval = (
    IntervalList
    & {
        "nwb_file_name": key["nwb_file_name"],
        "interval_list_name": key["interval_list_name"],
    }
).fetch1("valid_times")

valid_ephys_times = (
    IntervalList
    & {
        "nwb_file_name": key["nwb_file_name"],
        "interval_list_name": "raw data valid times",
    }
).fetch1("valid_times")
position_interval_names = (
    IntervalPositionInfo
    & {
        "nwb_file_name": key["nwb_file_name"],
        "position_info_param_name": "default_decoding",
    }
).fetch("interval_list_name")
valid_pos_times = [
    (
        IntervalList
        & {
            "nwb_file_name": key["nwb_file_name"],
            "interval_list_name": pos_interval_name,
        }
    ).fetch1("valid_times")
    for pos_interval_name in position_interval_names
]

intersect_interval = interval_list_intersect(
    interval_list_intersect(interval, valid_ephys_times), valid_pos_times[0]
)
valid_time_slice = slice(intersect_interval[0][0], intersect_interval[0][1])
valid_time_slice

from spyglass.common.common_interval import interval_list_intersect from spyglass.common import IntervalList key = {} key["interval_list_name"] = "02_r1" key["nwb_file_name"] = nwb_copy_file_name interval = ( IntervalList & { "nwb_file_name": key["nwb_file_name"], "interval_list_name": key["interval_list_name"], } ).fetch1("valid_times") valid_ephys_times = ( IntervalList & { "nwb_file_name": key["nwb_file_name"], "interval_list_name": "raw data valid times", } ).fetch1("valid_times") position_interval_names = ( IntervalPositionInfo & { "nwb_file_name": key["nwb_file_name"], "position_info_param_name": "default_decoding", } ).fetch("interval_list_name") valid_pos_times = [ ( IntervalList & { "nwb_file_name": key["nwb_file_name"], "interval_list_name": pos_interval_name, } ).fetch1("valid_times") for pos_interval_name in position_interval_names ] intersect_interval = interval_list_intersect( interval_list_intersect(interval, valid_ephys_times), valid_pos_times[0] ) valid_time_slice = slice(intersect_interval[0][0], intersect_interval[0][1]) valid_time_slice

Out[10]:

slice(1581886916.3153033, 1581888227.5987928, None)

In [11]:

from replay_trajectory_classification import ClusterlessClassifier
from replay_trajectory_classification.environments import Environment
from replay_trajectory_classification.continuous_state_transitions import (
    RandomWalk,
    Uniform,
)
from spyglass.decoding.clusterless import ClusterlessClassifierParameters

marks = marks.sel(time=valid_time_slice)
position_info = position_info.loc[valid_time_slice]

parameters = (
    ClusterlessClassifierParameters()
    & {"classifier_param_name": "default_decoding_gpu"}
).fetch1()

parameters["classifier_params"]["clusterless_algorithm_params"] = {
    "mark_std": 24.0,
    "position_std": 3.0,
    "block_size": int(2**13),
    "disable_progress_bar": False,
    "use_diffusion": False,
}
parameters["classifier_params"]["environments"][0] = Environment(
    place_bin_size=3.0
)


import cupy as cp

with cp.cuda.Device(0):
    classifier = ClusterlessClassifier(**parameters["classifier_params"])
    classifier.fit(
        position=position_info[["head_position_x", "head_position_y"]].values,
        multiunits=marks.values,
        **parameters["fit_params"],
    )
    results = classifier.predict(
        multiunits=marks.values,
        time=position_info.index,
        **parameters["predict_params"],
    )
    logging.info("Done!")

from replay_trajectory_classification import ClusterlessClassifier from replay_trajectory_classification.environments import Environment from replay_trajectory_classification.continuous_state_transitions import ( RandomWalk, Uniform, ) from spyglass.decoding.clusterless import ClusterlessClassifierParameters marks = marks.sel(time=valid_time_slice) position_info = position_info.loc[valid_time_slice] parameters = ( ClusterlessClassifierParameters() & {"classifier_param_name": "default_decoding_gpu"} ).fetch1() parameters["classifier_params"]["clusterless_algorithm_params"] = { "mark_std": 24.0, "position_std": 3.0, "block_size": int(2**13), "disable_progress_bar": False, "use_diffusion": False, } parameters["classifier_params"]["environments"][0] = Environment( place_bin_size=3.0 ) import cupy as cp with cp.cuda.Device(0): classifier = ClusterlessClassifier(**parameters["classifier_params"]) classifier.fit( position=position_info[["head_position_x", "head_position_y"]].values, multiunits=marks.values, **parameters["fit_params"], ) results = classifier.predict( multiunits=marks.values, time=position_info.index, **parameters["predict_params"], ) logging.info("Done!")

13-Sep-22 15:43:02 Fitting initial conditions...
13-Sep-22 15:43:02 Fitting continuous state transition...
13-Sep-22 15:43:04 Fitting discrete state transition
13-Sep-22 15:43:04 Fitting multiunits...
13-Sep-22 15:43:06 Estimating likelihood...

13-Sep-22 15:44:52 Estimating causal posterior...
13-Sep-22 15:48:34 Estimating acausal posterior...
13-Sep-22 16:00:30 Done!

In [16]:

from spyglass.decoding.visualization import create_interactive_2D_decoding_figurl


view = create_interactive_2D_decoding_figurl(
    position_info,
    marks,
    results,
    classifier.environments[0].place_bin_size,,
    position_name=["head_position_x", "head_position_y"],
    head_direction_name="head_orientation",
    speed_name="head_speed",
    posterior_type="acausal_posterior",
    sampling_frequency=500,
    view_height=800,
)

from spyglass.decoding.visualization import create_interactive_2D_decoding_figurl view = create_interactive_2D_decoding_figurl( position_info, marks, results, classifier.environments[0].place_bin_size,, position_name=["head_position_x", "head_position_y"], head_direction_name="head_orientation", speed_name="head_speed", posterior_type="acausal_posterior", sampling_frequency=500, view_height=800, )

If you want to view the decode in the jupyter notebook, uncomment and run this next cell. This will create an interactive visualization locally:

In [30]:

# view

# view

If you would like to create a visualization shareable in the cloud, run this next cell:

In [19]:

view.url(label="2D Decode Example")

view.url(label="2D Decode Example")

Out[19]:

'https://figurl.org/f?v=gs://figurl/spikesortingview-9&d=sha1://7251ae9794d4dfd783fabd9b84826c86b1982f74&label=2D%20Decode%20Example'